; oligo-analysis -type dna -l 3 -return occ,freq -v -format wc -1str -sort -i $RSAT/public_html/data/genomes/Caenorhabditis_briggsae.CB4.34/genome/Caenorhabditis_briggsae.CB4.34_stop_codons.wc -o $RSAT/public_html/data/genomes/Caenorhabditis_briggsae.CB4.34/genome/Caenorhabditis_briggsae.CB4.34_stop_codon_frequencies.tab ; Citation: van Helden et al. (1998). J Mol Biol 281(5), 827-42. ; Program version 1.169 ; Slow counting mode ; Oligomer length 3 ; Input file $RSAT/public_html/data/genomes/Caenorhabditis_briggsae.CB4.34/genome/Caenorhabditis_briggsae.CB4.34_stop_codons.wc ; Input format wc ; Output file $RSAT/public_html/data/genomes/Caenorhabditis_briggsae.CB4.34/genome/Caenorhabditis_briggsae.CB4.34_stop_codon_frequencies.tab ; Count overlapping matches ; Counted on a single strand ; Background model Bernoulli ; Background estimation method ; Sequence type DNA ; Nb of sequences 121838 ; Sum of sequence lengths 365514 ; discarded residues 65 (other letters than ACGT) ; discarded occurrences 29 (contain discarded residues) ; nb possible positions 121809 ; total oligo occurrences 121809 ; alphabet size 4 ; nb possible oligomers 64 ; oligomers tested for significance 0 ; ; column headers ; 1 seq oligomer sequence ; 2 id oligomer identifier ; 3 obs_freq observed relative frequency ; 4 occ observed occurrences #seq id obs_freq occ aag aag 0.1023898069929 12472 cag cag 0.0868655025491 10581 gag gag 0.0666453217743 8118 aaa aaa 0.0498567429336 6073 atg atg 0.0392663924669 4783 ttg ttg 0.0354981979985 4324 aat aat 0.0318449375662 3879 caa caa 0.0278715037477 3395 gaa gaa 0.0278550845997 3393 acg acg 0.0229293401965 2793 gat gat 0.0228144061605 2779 tcg tcg 0.0207538030852 2528 ttt ttt 0.0194238520963 2366 att att 0.0191529361541 2333 aga aga 0.0180200149414 2195 ctg ctg 0.0169856086168 2069 tgg tgg 0.0167721596926 2043 gtg gtg 0.0166982735266 2034 tag tag 0.0163124235483 1987 cat cat 0.0150645682996 1835 aac aac 0.0141450960110 1723 agg agg 0.0138659704948 1689 tat tat 0.0133077194624 1621 ttc ttc 0.0123964567479 1510 aca aca 0.0123882471739 1509 ccg ccg 0.0122815227118 1496 tca tca 0.0110747153330 1349 gcg gcg 0.0105493025967 1285 atc atc 0.0104672068566 1275 act act 0.0100074707123 1219 gtt gtt 0.0092686090519 1129 ctt ctt 0.0090633697017 1104 cca cca 0.0088335016296 1076 gct gct 0.0085625856874 1043 agt agt 0.0085625856874 1043 gga gga 0.0082424123012 1004 tct tct 0.0081767357092 996 tgt tgt 0.0078811910450 960 ggg ggg 0.0078237240270 953 gac gac 0.0078073048789 951 tga tga 0.0077087899909 939 ata ata 0.0076677421209 934 cga cga 0.0075610176588 921 taa taa 0.0072326346986 881 cgg cgg 0.0071505389585 871 tta tta 0.0068467847203 834 gca gca 0.0063131624100 769 cac cac 0.0062885336880 766 tac tac 0.0060832943379 741 ctc ctc 0.0060504560418 737 gtc gtc 0.0053280135294 649 cta cta 0.0050735167352 618 acc acc 0.0048764869591 594 tcc tcc 0.0047697624970 581 tgc tgc 0.0047615529230 580 agc agc 0.0044660082588 544 gcc gcc 0.0044003316668 536 gta gta 0.0035875838403 437 cct cct 0.0032345721581 394 cgt cgt 0.0031196381220 380 ggt ggt 0.0030047040859 366 cgc cgc 0.0024710817756 301 ccc ccc 0.0022165849814 270 ggc ggc 0.0020606030753 251 ; Host name n40 ; Job started 2017-04-15.082901 ; Job done 2017-04-15.082903 ; Seconds 2.49 ; user 2.49 ; system 0.11 ; cuser 0 ; csystem 0